What sort of moral issues result from creating a simulation universe that gives rise to sentient beings? I feel creeped out and reminded of Source Code with Jake Gyllenhaal for some reason.
The author has commented that he regrets having overlooked the moral implications of simulated life in his previous works (see e.g. http://gregegan.customer.netspace.net.au/PERMUTATION/FAQ/FAQ..., which contains spoilers for Permutation City) so I wouldn't be surprised if that was the inspiration for this story.